Our analysis revealed a linear, bifurcating progression pattern, originating from the normal samples, gradually shifting to state 1 with mixed ERG fusion–positive and –negative tumor samples, and diverging to two distinct trajectories to malignancy defined by the presence (referred to as ERG fusion–positive) or absence (ERG fusion–negative) of the ERG gene fusion (P < 3.8e–35, binomial test). Here, ERG is linked to neoplasm.